root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/bx/phylo/phast.py

"""
Rudimentary support for PHAST's tree model file format (a simple format for
storing trees and rate matrices).
"""

from numpy import *

class TreeModel:
    def __init__( self ):
        self.alphabet = None
        self.radix = 0
        self.order = 0
        self.subst_mod = None
        self.background = None
        self.tree = None
        self.matrix = None
    ## TODO: Need scipy for this method
    ## def matrix_for_time( self, t ):
    ##     return expm( self.matrix * t )
    ## matrix_for_time = cachedmethod( matrix_for_time )
    @staticmethod
    def from_file( f ):
        input = iter( f )
        tm = TreeModel()
        for line in input:
            if line.startswith( "ALPHABET:" ):
                tm.alphabet = tuple( line.split()[1:] )    
                tm.radix = len( tm.alphabet )
            if line.startswith( "ORDER:" ):
                tm.order = int( line.split()[1] )
            if line.startswith( "SUBST_MOD:" ):
                tm.subst_mod = line[11:].rstrip()                   
            if line.startswith( "BACKGROUND:" ):
                tm.background = tuple( map( float, line.split()[1:] ) )
            if line.startswith( "TREE:" ):
                tm.tree = line[6:].strip() 
            if line.startswith( "RATE_MAT:" ):
                matrix = zeros( (tm.radix,tm.radix), float )
                for i in range( len( tm.alphabet ) ):
                    matrix[i] = map( float, input.next().split() )
                tm.matrix = matrix
        return tm